Closed JianhuaWang95 closed 6 months ago
Hi Jianhua,
As far as a I know, it is not possible generate an allsites file without access to BAMs or gvcfs, apologies!
Kieran
Got it, thanks for the info!
Best, Jianhua
From: Kieran Samuk @.> Sent: Saturday, February 3, 2024 17:41 To: ksamuk/pixy @.> Cc: Wang, Jianhua @.>; Author @.> Subject: [EXTERNAL] Re: [ksamuk/pixy] How to generate a allsite vcf file based on the vcf file from 1000 Genomes Project (Issue #96)
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Hi Jianhua,
As far as a I know, it is not possible generate an allsites file without access to BAMs or gvcfs, apologies!
Kieran
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Hi Kieran,
I want to use pixy to calculate the pi values for some genes using the vcf file downloaded from 1000 Genomes Project. I do not have the bam file, is there any other way that I can use to generate a vcf file with both invariant and variant sites?
Thanks, Jianhua